I would say that in hindsight we all know that they should have stay clear of the ITCZ weather; well in that part of the world they could have deviated a hundred miles off course with no problem from ATC with respect to parallel airways.
However in the Atlantic or Pacific with closely spaced airways and random tracks, sometimes ATC is pretty slow or outright deny any request to deviate. I guess the junior crew members were reluctant to exercise the emegency option of deviating without clearance. Some airlines come down hard on pilots deviating without clearances.
You may say, ask for deviation clearance early, but with the modern flat plate weather radar system, severe weather returns sometimes only pop up within 40-60 miles ahead. ATC like Tokyo takes hours to reply or authorise deviations. How do you veterans deal with this situation........exercise your emergency contigency procedures and deviate without clearance and risk a TCAS event followed by loads of explaining to do?